ArticleJournal of biomedical semantics2016
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.
Article in Journal of biomedical semantics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Biological Magnetic Resonance Data Bank.Nucleic acids research · 2023Article
- The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science.RSC advances · 2021Review
- Deconstructing the STAR File Format.Balisage series on markup technologies · 2021Article
- NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments.Journal of biomolecular NMR · 2019Review
- New tools and functions in data-out activities at Protein Data Bank Japan (PDBj).Protein science : a publication of the Protein Society · 2018Article
- Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.Nucleic acids research · 2017Article
- Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.Methods in molecular biology (Clifton, N.J.) · 2017Review
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
backgroundThe nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases.
findingsTo enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes.
conclusionsWe have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.